Actually, it now works when I re-source my .bash_profile and .bashrc files. Not sure why that would be. Chris
Chris Watson wrote: > Yes, the same error. > Chris > > Anastasia Yendiki wrote: > >> When you run that bet command line outside of trac-all, does it give >> you the same error? >> >> On Wed, 15 Feb 2012, Chris Watson wrote: >> >> >>> Here's output from mri_info: >>> [freesurfer@occipital dmri]$ mri_info lowb.nii.gz >>> Volume information for lowb.nii.gz >>> type: nii >>> dimensions: 96 x 96 x 56 >>> voxel sizes: 2.5000, 2.5000, 2.5000 >>> type: FLOAT (3) >>> fov: 240.000 >>> dof: 0 >>> xstart: -120.0, xend: 120.0 >>> ystart: -120.0, yend: 120.0 >>> zstart: -70.0, zend: 70.0 >>> TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: >>> 0.00 degrees >>> nframes: 1 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = >>> 0.9450 >>> : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = >>> 31.8560 >>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = >>> 25.3936 >>> Orientation : LAS >>> Primary Slice Direction: axial >>> >>> voxel to ras transform: >>> -2.5000 0.0000 0.0000 120.9450 >>> 0.0000 2.5000 0.0000 -88.1440 >>> 0.0000 0.0000 2.5000 -44.6064 >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> voxel-to-ras determinant -15.625 >>> >>> ras to voxel transform: >>> -0.4000 0.0000 0.0000 48.3780 >>> -0.0000 0.4000 -0.0000 35.2576 >>> -0.0000 -0.0000 0.4000 17.8426 >>> 0.0000 0.0000 0.0000 1.0000 >>> >>> It looks normal in fslview/freeview. >>> Chris >>> >>> Anastasia Yendiki wrote: >>> >>>> Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first >>>> guess, too. Does this lowb.nii.gz actually exist? Anything looks >>>> strange >>>> when you run mri_info/freeview/fslview on it? >>>> >>>> a.y >>>> >>>> On Wed, 15 Feb 2012, Chris Watson wrote: >>>> >>>> >>>> >>>>> Hello, in running trac-all -prep, I get an error saying that it >>>>> >>>> can't >>>> >>>>> open "lowb.nii.gz.hdr": >>>>> >>>>>> fslroi >>>>>> >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz >>>> >>>> >>>> >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >>>> >>>> >>>> >>>>> 0 1 >>>>> fslmaths >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >>>> >>>> >>>> >>>>> -Tmean >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >>>> >>>> >>>> >>>>> bet >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >>>> >>>> >>>> >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz >>>> >>>> >>>> >>>>> -m -f 0.3 >>>>> Can't open >>>>> >>>>> >>>> /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr >>>> >>>> >>>> >>>>> Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue >>>>> >>>> Jan 10 >>>> >>>>> 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>>> trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 >>>>>> The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't >>>>>> >>>> encounter this >>>> >>>>> problem with other subjects that I am processing. Any thoughts? >>>>> >>>>>> Thanks, >>>>>> >>>>> Chris >>>>> >>>>>> _______________________________________________ >>>>>> >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>> you in >>>> error >>>> but does not contain patient information, please contact the sender >>>> and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>> >>> >>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
